Long story short - QuickBooks started recording our VAT on the VAT100 incorrectly a long time ago (I think I have figured out why while trying to solve this problem). Every time I tried to "File a VAT Return" through QB it was showing ridiculous figures that were completely incorrect. At the time I spoke to our accountant and she suggested using the "VAT Detail Report" to find the accurate figures and submit them manually to the HMRC website. This is what I have done ever since.

To record a payment for VAT to HMRC I have been posting directly to the VAT Control account (something QB warns you about doing but I was told to ignore by the accountant - we have now changed accountants by the way but the new one hasn't picked this up either). I have now realised this is incorrect and the payments (every one since the company began in 2005 and before I started here) should have been put through a Suspense account (I think? Please correct me if I am wrong).

Since we are about to hit the MTD deadline I thought I better check this VAT100 and see what is reporting etc. However it seems to now be reporting EVERYTHING we have ever done on the VAT100 (so £11m + turnover) and saying we owe £1.5m in VAT. I can assure you we don't! It even shows a different figure on the Balance Sheet so I am very confused where we stand. 

We had a VAT inspection last year (he didn't pick this up either) and he was happy with the way I had been doing things. He agreed we had being reporting VAT correctly including the Duty on imports that I was worried about. He failed to mention the MTD deadline however and this has crept up on me unknowingly.

Am I going to have to go back over nearly 14 years worth of payments and change them? At the moment I don't see any alternative!! Any help would be appreciated. 

I'm using QB Desktop Premier 2019 if that makes any difference?